Guarding Reproducibility

That title sure is dramatic…

Gabriel Mateus Bernardo Harrington

Research Associate | Webber Group

2024-01-19

Questions

Menti meter link here

https://www.mentimeter.com/app/presentation/alrcqg7tuw6z221zusbii9tmi788qrkc/71g4gjj8tber/edit

Discussion groups

  • Each table has a topic to discuss for 10 minutes
  • Please add your thoughts on the topic to the shared Google Doc
    • Link here

Code Review

  • Join!
    • https://github.com/orgs/UKDRI/teams/code-review
  • How does community want it to be used?
    • Quick second pair of eyes on code snippet?
    • Methodological advice (QC cutoff, etc)?
    • Full review of project codebase?
  • Acknowledgements for review?
    • GitHub has metrics
    • Authorship? Establish group rules, or discuss ad-hoc?
    • Minimal acknowledgement in GitHub Contributors file for reviewers?

Proposed workflow

  1. Make a repo on DRI GitHub Org (perhaps using the template!)
  2. Write and publish a registered report outlining the project
  3. Gather/analyse data
  • Make ADDI workspace?
  • Use existing pipelines if applicable (Nextflow)
  • Containerise software environment
  1. Publish all the things!
  • Pre-print -> diamond open access
  • Data on relevant public repositories + ADDI?
  • generate DOI for code repo via Zenodo

Example slide

Here is some text. The font is Arial (hex: #00326e). Here is another sentence with bold and italic text. Here is an example reference: (Baker and Escott-Price 2020)

  • Here is a bullet point
  • The font used is Arial and font size is 18px
  • Bullets are coloured hex: #0ac8ff

Incremental content

Hi!

Use . . . to separate content as an incremental slide!

Diagrams with Mermaid!

Read about how to create a diagram in this post by Mine Çetinkaya-Rundel.

flowchart LR
  A[qmd] --> B(Knitr)
  A[qmd] --> C(Jupyter)
  B(Knitr) --> D[md]
  C(Jupyter) --> D[md]
  D[md] --> E(pandoc)
  E(pandoc) --> F(HTML)
  E(pandoc) --> G(PDF)
  E(pandoc) --> H(Word)
  E(pandoc) --> I{and more}
Figure 1: How Quarto orchestrates rendering of documents: start with a qmd file, use the Knitr or Jupyter engine to perform the computations and convert it to an md file, then use Pandoc to convert to various file formats including HTML, PDF, and Word.

Exporting into PDF

You can use the function pagedown::chrome_print() to print the HTML version into a PDF!

pagedown::chrome_print("path-to-file.html")

Thanks for listening

Replace profile.png with the path to the pictures you’d like to use.

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References

UKDRI theme for Quarto Presentations. Code available on GitHub.

Baker, Emily, and Valentina Escott-Price. 2020. “Polygenic Risk Scores in Alzheimer’s Disease: Current Applications and Future Directions.” Frontiers in Digital Health 2: 14. https://doi.org/10.3389/fdgth.2020.00014.